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Forum: Bioinformatics 07-04-2016, 06:24 AM
Replies: 0
Views: 868
Posted By sampie
Database of human gut bacteria

Hi,

I have a list of bacteria (from cazy.org) and I need to know which of those are human gut bacteria, so that I could filter the list.

Is somewhere an online database, from which I could get...
Forum: General 10-07-2014, 05:06 AM
Replies: 3
Views: 2,088
Posted By sampie
Hi, I tried to isolate a ref sequence and...

Hi,

I tried to isolate a ref sequence and try with that. So, I have ref.fasta with only one sequence. I have also sorted.bam which is an alignment against the ref.fasta. It seems samtools is not...
Forum: General 10-04-2014, 10:21 AM
Replies: 3
Views: 2,088
Posted By sampie
Thanks for reply! UGENE looks like a good tool....

Thanks for reply! UGENE looks like a good tool. However, I was unable to find out how to build consensus sequence with UGENE command line. Can I have an example of a command that can be used to build...
Forum: General 10-03-2014, 06:13 AM
Replies: 3
Views: 2,088
Posted By sampie
How to generate consensus sequence for all refs

Hi,

I have been trying to use samtools to create consensus sequences. However, it seems that conseqs.fastq (see command below) is missing consensus sequences for most reference sequences.

---...
Forum: Bioinformatics 08-23-2014, 11:26 PM
Replies: 0
Views: 1,236
Posted By sampie
RDP II - taxonomy

Hi,

I have RDP II release11_2_Bacteria_unaligned.gb. The file has taxonomy written, for example, like:

SOURCE Agromyces ramosus
ORGANISM Agromyces ramosus
Root; Bacteria;...
Forum: Bioinformatics 08-15-2014, 05:35 AM
Replies: 5
Views: 1,665
Posted By sampie
Thanks for replies. I took a look at SAM...

Thanks for replies.

I took a look at SAM format specification. It was more clear to me than bowtie2 manual.

I am now testing bits 0x1, 0x2 and 0x8 from flags and if they are on I am determining...
Forum: Bioinformatics 08-14-2014, 06:07 AM
Replies: 5
Views: 1,665
Posted By sampie
Bowtie2 output with paired end reads

Hi,

I am trying to use bowtie2 to align paired end Illumina read files.

I am using following command:

./bowtie2 -a --threads 8 --n-ceil 42 --very-sensitive-local --quiet --no-sq --no-hd...
Forum: Bioinformatics 06-10-2014, 11:40 AM
Replies: 5
Views: 2,007
Posted By sampie
Thanks for suggestion. How about bowtie2?...

Thanks for suggestion.

How about bowtie2? It seem to be quite popular and good tools. From bowtie2 help I found that it can be disabled that N is considered as a negatively scoring match....
Forum: Bioinformatics 06-04-2014, 11:11 PM
Replies: 5
Views: 2,007
Posted By sampie
Hi, It seems it might be possible to get...

Hi,

It seems it might be possible to get blast to work for some data set by trying various parameters. However, I contacted ncbi support and they told that handling ambiguous matches is not the...
Forum: Bioinformatics 06-02-2014, 07:42 AM
Replies: 5
Views: 2,007
Posted By sampie
ncbi-blast

Hi,

I have a trialseq.fa file having a sequence:

>trialseq
TGGCCTAACCTTCGGGAAGGAGCCGTCTAAGGCAGGGCAGATGACNNNNNNNNNNNNGTAACAAGNNNNNNNNNNNNGAACCTGNNNNNNGATCACCTCCTTTCTA

There is also a blast...
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